5mC interactions in PDB entry 4R2A auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

Summary information and primary citation [schematics · contacts · top · homepage · tutorial]

PDB-id

4R2A

Class

DNA binding protein-DNA

Method

X-ray (1.59 Å)

Summary

Egr1-zif268 zinc fingers in complex with methylated DNA
List of 2 5mC-amino acid contacts:

B.5CM9: stacking-with-A.ARG351 is-WC-paired is-in-duplex [+]:GcG/cGC

C.5CM3: other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG

direct SNAP output · DNAproDB 2.0

Reference

Hashimoto, H., Olanrewaju, Y.O., Zheng, Y., Wilson, G.G., Zhang, X., Cheng, X.: (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313.

Abstract

In mammalian DNA, cytosine occurs in several chemical forms, including unmodified cytosine (C), 5-methylcytosine (5 mC), 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5 fC), and 5-carboxylcytosine (5 caC). 5 mC is a major epigenetic signal that acts to regulate gene expression. 5 hmC, 5 fC, and 5 caC are oxidized derivatives that might also act as distinct epigenetic signals. We investigated the response of the zinc finger DNA-binding domains of transcription factors early growth response protein 1 (Egr1) and Wilms tumor protein 1 (WT1) to different forms of modified cytosine within their recognition sequence, 5'-GCG(T/G)GGGCG-3'. Both displayed high affinity for the sequence when C or 5 mC was present and much reduced affinity when 5 hmC or 5 fC was present, indicating that they differentiate primarily oxidized C from unoxidized C, rather than methylated C from unmethylated C. 5 caC affected the two proteins differently, abolishing binding by Egr1 but not by WT1. We ascribe this difference to electrostatic interactions in the binding sites. In Egr1, a negatively charged glutamate conflicts with the negatively charged carboxylate of 5 caC, whereas the corresponding glutamine of WT1 interacts with this group favorably. Our analyses shows that zinc finger proteins (and their splice variants) can respond in modulated ways to alternative modifications within their binding sequence.

Base-block schematics in six views [summary · contacts · top · homepage · tutorial]

The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model, with the methyl-carbon atom in black.
Watson-Crick base pairs are represented as long rectangular blocks with the minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code by chain identifier.
The block schematics were created with 3DNA-DSSR, and images were rendered using PyMOL.
Download the PyMOL session file corresponding to the top-left image in the following panel.

List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

The contacts include paired nucleotides (mostly a G in G-C pairing), and amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
The structure is oriented in the 'standard' base reference frame of 5mC, allowing for easy comparison and direct superimposition between entries.
The black sphere (•) denotes the 5-methyl carbon atom in 5mC.

	No. 1 B.5CM9: download PDB file for the 5mC entry stacking-with-A.ARG351 is-WC-paired is-in-duplex [+]:GcG/cGC
	No. 2 C.5CM3: download PDB file for the 5mC entry other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG